Figure 2. The somatic OncoPanel (BWH Pathology, Boston, MA, USA.) profile obtained from the retroperitoneal lymph node biopsy showed multiple copy number changes consistent with the patient’s RCC. (A) An all chromosome view of the sample copy number plot. Each contiguously baited segment is represented by a dot, the read counts were normalized against a panel of normal samples and the log2 ratios were plotted. (B) One single-copy loss in 3p encompassing 3p25.3 where the VHL gene resides on the chromosome. (C) Single-copy gain along chromosome 5 encompassing 5q22.2 where the APC gene resides on the chromosome. (D) Single-copy gain of a part of 16p. Axis labels and descriptions: Nucleotide position of baited regions (×1000) (X-axis); log2 ratio (Y-axis, left). % GC, graphical representation of the GC content of each segment in blue (Y-axis, right). The vertical line in each panel delineates the position of the centromere in each chromosome. Copy number calls were made using an adaptive calling method that adjusts the threshold per sample. For 3p, chromosome 5, and 16p, the average log2 ratios were −0.38, 0.26, and 0.34, respectively. Gains and losses were called respectively, using thresholds of 0.25 and −0.32.